Protein Reliability Report Panel

Display a simple graphical representation of various metrics that indicate the reliability or quality of a protein structure, and in particular, X-ray structures of proteins.

To open this panel: click the Tasks button and browse to Biologics → Structure Reliability Report.
To open this panel from the entry group for the results of a homology modeling job, use the Workflow Action Menu .

  • Using
  • Features
  • Additional Resources

Using the Protein Reliability Report Panel

To analyze a protein for reliability, you must first display it in the Workspace. If a report has already been generated for a protein, and it is displayed in the Workspace, the report is displayed immediately.

The metrics that are used to assess the quality of the protein structure are described below, with the cutoff values for marking a problem. Some metrics require X-ray reflection data for their evaluation. Some apply to the entire protein, others apply to the region that is analyzed.

Protein reliability metrics.
Metric Description Cutoff
Backbone dihedrals Number of residues that are considered Ramachandran outliers, i.e. have an unlikely phi and psi dihedral angle. 1
Binding site packing Number of contiguous binding site residue stretches of length 3 that all have Z-scores less than −4.0. The Z-score is based on the Directional atomic contact analysis as reported in [1]. 0
Binding site RSCC Average Real Space Cross Correlation (RSCC) coefficients of residues in the binding site. The RSCC is calculated by generating a simulated electron density map and comparing it to an omit map where the binding site residues have been omitted. 0.9
Bond angle deviations Number of bond angles in the analyzed region that deviate more than 10° from their ideal value. 1
Bond length deviations Number of bond lengths in the analyzed region that deviate by more than 0.25A from their ideal value. 1
Buried unsatisfied acceptor Number of buried H-bond acceptors in the analyzed region that are not part of a hydrogen bond. 1
Buried unsatisfied donor Number of buried H-bond donors in the analyzed region that are not part of a hydrogen bond. 1
Improper torsions Number of residues where the Root Mean Square deviation of all improper torsions exceed 10°. 0
Isolated water clusters Number of water clusters that form no interactions with non-water molecules. 0
Ligand RSCC Average Real Space Cross Correlation (RSCC) coefficients of all selected ligands. The RSCC is calculated by generating a simulated electron density map and comparing it to an omit map where the ligands have been omitted. 0.9
Missing atoms Number of atoms missing from the analyzed region. 0
Missing loops Number of loops missing from the entire structure. 0
Non-binding-site packing Number of contiguous non-binding site residue stretches of length 3 that all have Z-scores less than −4.0. The Z-score is based on the Directional atomic contact analysis as reported in [1]. 0
PDB resolution Reported X-ray structure resolution, taken from the input structure file. 2.5 Å
PDB Rfree-R Difference between R factors for the unfitted X-ray data (used for cross-validation, R-free) and the fitted X-ray data (R-work). The R-factors are taken from the input structure file. 0.06
Peptide planarity Number of omega-dihedral angles that deviate more than 20° from their 180° trans-form. Cis-peptides where the second residue is a proline are not reported. 0
Protein packing Packing environment of the protein calculated as given in [1], where the global Z-score is averaged over all protein residue Z-scores. A problem is flagged if the global Z-score is lower than -1.2. High-quality structures have a uniform distribution of atoms in the core of the protein. The presence of holes in the core can be an indicator of poorly built side chains or backbone, or incorrect threading of the sequence through the density. −1.2
Side-chain dihedrals Number of residues with unlikely side chain dihedral angles, using only the chi-1 and chi-2 angles. 0
Side-chain planarity Number of side chains that are expected to be planar whose RMSD to the ideal plane exceeds 0.5Å. 0
Steric clashes Number of abnormally short interatomic distances. 1
Unusual B-factors Number of residues in the analyzed region where the backbone or sidechain has an average B-factor larger than 100 or is negative. 100
Waters with no HB partners Number of waters that do not form hydrogen bonds at all. 0

For a detailed description of the metrics referred to by [1] above, see Vriend, G., and C. Sander. "Quality control of protein models: directional atomic contact analysis." Journal of applied crystallography 26.1 (1993): 47-60.

A PDF report can be generated using the structure_reliability Command Help utility.

Protein Reliability Report Panel Features

Analyze option menu and tools

Choose the part of the protein to analyze from this option menu. There are three choices:

  • Entire structure—Analyze the entire structure that is in the Workspace.

  • Region around ligand—Analyze the region that includes the ligand and all residues that have atoms within a specified distance of the ligand. The default distance is 10 Å, and can be changed in the Shell text box.

    When you choose this option, a text box and a Pick ligand option are displayed to the left of the menu. To identify the ligand, select the Pick ligand option and pick a ligand atom in the Workspace. The identity of the ligand is displayed in the text box.

  • Custom region—Analyze the region that includes a selected set of residues.

    When you choose this option, a text box and a Select button are displayed to the left of the menu. To select the residues that define the region, click Select and use the tools in the Atom Selection dialog box. The ASL expression for these residues is displayed in the text box.

Use diffraction data option, text box and Browse button

If you want to include X-ray diffraction data in the analysis, select this option and click Browse. A file selector opens, in which you can locate and select the file that contains the diffraction data. The file name is displayed in the text box. You can also type the full file name into the text box. The X-ray data are used to calculate real-space R-factors and correlation coefficients.

Display results for chain option menu

The results of the analysis can be displayed for each chain separately, or for the entire protein. Use this option menu to select the chain or the entire protein (All).

Display area

This area displays a visual representation of the metrics for protein reliability. For each metric a circle is drawn that represents the quality of that metric. It is colored red if the deviation from acceptable values is larger than a cutoff, green if the deviation is smaller. For counts, the color is yellow if the cutoff is exceeded by one. The radius of the circle indicates the magnitude of the metric. Circles are still drawn for metrics that were not calculated, but they are not colored. For large deviations, the circles can overlap other circles.

The intention of the display is to provide a quick means of determining if the protein structure is reliable, and which aspects of the structure deviate from acceptable values.

If you click on the title of a metric, the values for that metric are displayed in a table, to the right.

Results table

For metrics whose values lie outside acceptable ranges, the unacceptable values are displayed in a table in this section. The section is blank initially, and is cleared if you choose a metric whose values are all acceptable.

Information area

This area displays an informational message on metrics whose values lie outside the acceptable range, when you click on the metric in the display area. It specifies the cutoff for acceptable values, and suggests possible reasons that the values might lie outside the range.

Save Report button

Save a copy of the report in a text file (.txt). The report lists metrics and their values.

Save Image button

Save an image of the display area to a file, in PNG, JPEG, or TIFF format. Opens a file selector, in which you can choose the image format and save the file.

Job toolbar

Manage job submission and settings. See Job Toolbar for a description of this toolbar.

The Job Settings button opens the Protein Reliability Report - Job Settings Dialog Box, where you can make settings for running the job.

Status bar

The status bar displays information about the current job settings and status for the panel. The settings includes the job name, task name and task settings (if any), number of subjobs (if any) and the host name and job incorporation setting. The job status can include messages about job start, job completion and incorporation.

Use the Reset button to reset the panel to its default settings and clear any data from the panel. You can also reset the panel from the Job toolbar.

The status bar also contains the Help button , which opens the help topic for the panel in your browser. If the panel is used by one or more tutorials, hovering over the Help button displays a button, which you can click to display a list of tutorials (or you can right-click the Help button instead). Choosing a tutorial opens the tutorial topic.

Tutorials

Quick Reference Sheets

Videos

Related Topics